Just rebooted and yes the pop up was there again. Also i had trouble with the start up again with a error message "windows failed to start up". I had to log in under F8 - Last know good config to get back in. The repair failed to fix this issue before and advance settings said there was a "Root Causes - 1" and it was System Disk/device/hard disk just FYI

Please Boot to the System Recovery Options
If you have Windows 7 installation disc, just insert a DVD to the drive, restart computer and it should load automatically (option two presented in the article).
It's possible also that your computer has a pre-installed recovery partition instead - in such a case use a method one (by pressing F8 before Windows starts loading)...

On the System Recovery Options menu you will get the following options:

Startup Repair

System Restore

Windows Complete PC Restore

Windows Memory Diagnostic Tool

Command Prompt

Choose Command Prompt
You should see X:\SOURCES>...

Execute the following commands in bold.
Press Enter after every one of them.

I don't have the Windows 7 installation disk and looks like i don't have a pre-installed recovery partition as when i pressed F8 i didn't get those options. I have been able to reboot a number of times without any issues recently.